Re: [Rdkit-discuss] remove salts + neutralize

[Chris E. <cge...@gm...>]

The minuses are right. These are the single bonds between the individual
aromatic rings and this representation is strictly correct. The OpenBabel
representation doesn't mark these bonds as explicitly single and, as
they're between two aromatic atoms, the bond type could be inferred to be
aromatic. In principle this could cause problems elsewhere.

In short, RDKit is explicit and correct, OpenBabel is probably OK but
relies on any software reading its SMILES interpreting the ambiguity
correctly.

Best regards,
Chris

Chris

On 14 March 2018 at 15:40, Mario Lovrić <mar...@gm...> wrote:

> Dear all,
>
>
> I was trying to remove salts + neutralize several structures:
>
> O.[K+].NC(=O)C1=NC(=N[N-]1)C1=CC=CC(=C1)C1=CC(F)=CC=C1OCC(F)(F)C(F)(F)F
>
> -->remove salts-->
>
> NC(=O)c1nc(-c2cccc(-c3cc(F)ccc3OCC(F)(F)C(F)(F)F)c2)n[n-]1
>
> --> neutralize-->
>
> NC(=O)c1nc(-c2cccc(-c3cc(F)ccc3OCC(F)(F)C(F)(F)F)c2)n[nH]1
>
>
> The minuses appear front of the "c"s.
> I guess it is considered as bonds everywhere.
>
> When canonicalizing them in RDKit they dont change, but OpenBabel does for
> example.
>
> Fc1ccc(c(c1)c1cccc(c1)c1n[nH]c(n1)C(=O)N)OCC(C(F)(F)F)(F)F
>
>
> Might it cause problems anywhere?
>
>
> KR
> --
> Mario Lovrić
>
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